SAXSdb — 4jwj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

tRNA (guanine(9)-N1)-methyltransferase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 84–276	Fragment：UNP RESIDUES 84-276	SO4 SULFATE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；1.5M Lithium sulfate monohydrate, 0.1M BIS-TRIS propane, pH 7.0, vapor diffusion, hanging drop, temperature 287K	Resolution 1.76 Å R-free 0.251
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 84–276	Fragment：UNP RESIDUES 84-276	SO4 SULFATE ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；1.5M Lithium sulfate monohydrate, 0.1M BIS-TRIS propane, pH 7.0, vapor diffusion, hanging drop, temperature 287K	Resolution 1.76 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4JWJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XZQ Trm10-tRNA complex (closed conformation) Deposited 2025-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–293（293 aa）	Not recorded	AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.63 Å
9XZR Trm10-tRNA complex (open conformation) Deposited 2025-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–293（293 aa）	Not recorded	AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9XZS Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA) Deposited 2025-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain B 1–293（293 aa） Chain C 1–293（293 aa）	Not recorded	AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRM10_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–202； UniProt 84–276 Author chain B； PDBConstruct 10–202； UniProt 84–276

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4jwj
Deposition date deposition_date	2013-03-27
Structure title title	Crystal structure of scTrm10(84)-SAH complex
Keywords keywords	tRNA MTase domain, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.59 Å
Radius of gyration Rg (electron density) rg_electron	23.54 Å
Forward intensity I(0) i0	38360200.00
Molecular weight molecular_weight	46772.0 kDa
Excluded volume excluded_volume	58274 Å³
Envelope volume envelope_volume	69972 Å³
Hydration-shell volume shell_volume	25267 Å³
Envelope diameter envelope_diameter	84.4 Å
Shell Rg shell_rg	30.23 Å
Envelope Rg envelope_rg	23.84 Å
Shape Rg shape_rg	23.58 Å
Total Rg total_rg	24.24 Å
Total atoms total_atoms	3281
Residues n_residues	386
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.2 Å
Rg (real space) rg_real	24.66 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	3.8360e+07
I(0) uncertainty (real space) i0_real_error	5.7910e+05
Rg (reciprocal space) rg_reciprocal	24.64 Å
I(0) (reciprocal space) i0_reciprocal	38360000.0000
Solution quality estimate total_estimate	0.8727
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.446
Kurtosis Kurtosis kurtosis	-0.306
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11460000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	tRNA (guanine(9)-N1)-methyltransferase
Molecular weight formula_weight	23907.4 kDa
EC 编号 ec_number	2.1.1.221
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3641

MGHHHHHHMPRINVNQTDSGIEIILDCSFDELMNDKEIVSLSNQVTRAYSANRRANHFAEIKVAPFDKRLKQRFETTLKNTNYENWNHFKFLPDDKIMFGDEHISKDKIVYLTADTEEKLEKLEPGMRYIVGGIVDKNRYKELCLKKAQKMGIPTRRLPIDEYINLEGRRVLTTTHVVQLMLKYFDDHNWKNAFESVLPPRK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	328

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4jwjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4jwjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	131.583 Å
Unit-cell length b length_b	58.861 Å
Unit-cell length c length_c	99.767 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	37.570 Å
R factor r_factor	0.2195
R_work r_work	0.2178
R_free r_free	0.2510

fit	/app/data/saxs_computation/jw/4jwj/4jwj.fit
pddf	/app/data/pr_computation/jw/4jwj/4jwj.pr.out
profile	/app/data/saxs_computation/jw/4jwj/4jwj.dat

Crystal structure of scTrm10(84)-SAH complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

tRNA (guanine(9)-N1)-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction